PDBsum entry 9ca2

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protein metals links
Lyase(oxo-acid) PDB id
Protein chain
255 a.a. *
Waters ×76
* Residue conservation analysis
PDB id:
Name: Lyase(oxo-acid)
Title: Engineering the hydrophobic pocket of carbonic anhydrase ii
Structure: Carbonic anhydrase ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
2.80Å     R-factor:   0.180    
Authors: R.S.Alexander,D.W.Christianson
Key ref:
R.S.Alexander et al. (1991). Engineering the hydrophobic pocket of carbonic anhydrase II. Biochemistry, 30, 11064-11072. PubMed id: 1932029 DOI: 10.1021/bi00110a008
09-Jul-91     Release date:   15-Jul-92    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00918  (CAH2_HUMAN) -  Carbonic anhydrase 2
260 a.a.
255 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular space   11 terms 
  Biological process     angiotensin-mediated signaling pathway   22 terms 
  Biochemical function     protein binding     5 terms  


    Added reference    
DOI no: 10.1021/bi00110a008 Biochemistry 30:11064-11072 (1991)
PubMed id: 1932029  
Engineering the hydrophobic pocket of carbonic anhydrase II.
R.S.Alexander, S.K.Nair, D.W.Christianson.
Wild-type and mutant human carbonic anhydrases II, where mutations have been made in the hydrophobic pocket of the active site, have been studied by X-ray crystallographic methods. Specifically, mutations at Val-143 (the base of the pocket) lead to significant changes in catalytic activity and protein structure. The obliteration of a well-defined pocket in the Val-143----Phe and Val-143----Tyr mutants results in significantly diminished enzyme activity [(5 x 10(4))-fold and (3 x 10(5))-fold, respectively]; however, the activity of the Val-143----His mutant is diminished less (10(2)-fold), and deepening the pocket in the Val-143----Gly mutant results in only a 2-fold decrease in activity [Fierke et al., 1991 (preceding paper in this issue)]. These results indicate that the hydrophobic pocket is important for substrate association with the enzyme, but there are probably several catalytically acceptable substrate trajectories through this region of the enzyme structure. Additionally, each mutant protein exhibits long-range (ca. 10-15 A) compensatory structural changes which accommodate the Val-143 substitution. As such, the genetic-structural approach represented in this work serves as a three-dimensional paradigm for the redesign of specificity pockets in other protein catalysts.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20300744 H.M.Becker, M.Klier, and J.W.Deitmer (2010).
Nonenzymatic augmentation of lactate transport via monocarboxylate transporter isoform 4 by carbonic anhydrase II.
  J Membr Biol, 234, 125-135.  
19679198 J.F.Domsic, and R.McKenna (2010).
Sequestration of carbon dioxide by the hydrophobic pocket of the carbonic anhydrases.
  Biochim Biophys Acta, 1804, 326-331.  
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
19459702 R.S.Rowlett, C.Tu, J.Lee, A.G.Herman, D.A.Chapnick, S.H.Shah, and P.C.Gareiss (2009).
Allosteric site variants of Haemophilus influenzae beta-carbonic anhydrase.
  Biochemistry, 48, 6146-6156.
PDB codes: 3e1v 3e1w 3e24 3e28 3e2a 3e2w
18539591 H.M.Becker, and J.W.Deitmer (2008).
Nonenzymatic proton handling by carbonic anhydrase II during H+-lactate cotransport via monocarboxylate transporter 1.
  J Biol Chem, 283, 21655-21667.  
18768466 J.F.Domsic, B.S.Avvaru, C.U.Kim, S.M.Gruner, M.Agbandje-McKenna, D.N.Silverman, and R.McKenna (2008).
Entrapment of Carbon Dioxide in the Active Site of Carbonic Anhydrase II.
  J Biol Chem, 283, 30766-30771.
PDB codes: 3d92 3d93
18335973 V.M.Krishnamurthy, G.K.Kaufman, A.R.Urbach, I.Gitlin, K.L.Gudiksen, D.B.Weibel, and G.M.Whitesides (2008).
Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding.
  Chem Rev, 108, 946.  
  17664347 A.Weise, H.M.Becker, and J.W.Deitmer (2007).
Enzymatic suppression of the membrane conductance associated with the glutamine transporter SNAT3 expressed in Xenopus oocytes by carbonic anhydrase II.
  J Gen Physiol, 130, 203-215.  
17353189 H.M.Becker, and J.W.Deitmer (2007).
Carbonic anhydrase II increases the activity of the human electrogenic Na+/HCO3- cotransporter.
  J Biol Chem, 282, 13508-13521.  
12056894 S.Huang, B.Sjöblom, A.E.Sauer-Eriksson, and B.H.Jonsson (2002).
Organization of an efficient carbonic anhydrase: implications for the mechanism based on structure-function studies of a T199P/C206S mutant.
  Biochemistry, 41, 7628-7635.
PDB codes: 1lg5 1lg6 1lgd
11371461 M.Persson, J.R.Harbridge, P.Hammarström, R.Mitri, L.G.Mårtensson, U.Carlsson, G.R.Eaton, and S.S.Eaton (2001).
Comparison of electron paramagnetic resonance methods to determine distances between spin labels on human carbonic anhydrase II.
  Biophys J, 80, 2886-2897.  
11371460 P.Hammarström, R.Owenius, L.G.Mårtensson, U.Carlsson, and M.Lindgren (2001).
High-resolution probing of local conformational changes in proteins by the use of multiple labeling: unfolding and self-assembly of human carbonic anhydrase II monitored by spin, fluorescent, and chemical reactivity probes.
  Biophys J, 80, 2867-2885.  
11076507 J.D.Cox, J.A.Hunt, K.M.Compher, C.A.Fierke, and D.W.Christianson (2000).
Structural influence of hydrophobic core residues on metal binding and specificity in carbonic anhydrase II.
  Biochemistry, 39, 13687-13694.
PDB codes: 1fql 1fqm 1fqn 1fqr 1fr4 1fr7 1fsn 1fsq 1fsr
10480931 A.J.Pommer, U.C.Kühlmann, A.Cooper, A.M.Hemmings, G.R.Moore, R.James, and C.Kleanthous (1999).
Homing in on the role of transition metals in the HNH motif of colicin endonucleases.
  J Biol Chem, 274, 27153-27160.  
10336637 B.Elleby, B.Sjöblom, and S.Lindskog (1999).
Changing the efficiency and specificity of the esterase activity of human carbonic anhydrase II by site-specific mutagenesis.
  Eur J Biochem, 262, 516-521.  
10872443 D.W.Christianson, and J.D.Cox (1999).
Catalysis by metal-activated hydroxide in zinc and manganese metalloenzymes.
  Annu Rev Biochem, 68, 33-57.  
9164450 M.L.Mansfield (1997).
Fit to be tied.
  Nat Struct Biol, 4, 166-167.  
9336012 S.Lindskog (1997).
Structure and mechanism of carbonic anhydrase.
  Pharmacol Ther, 74, 1.  
8639494 C.C.Huang,, C.A.Lesburg, L.L.Kiefer, C.A.Fierke, and D.W.Christianson (1996).
Reversal of the hydrogen bond to zinc ligand histidine-119 dramatically diminishes catalysis and enhances metal equilibration kinetics in carbonic anhydrase II.
  Biochemistry, 35, 3439-3446.
PDB codes: 1zsa 1zsb 1zsc
8987973 J.E.Jackman, K.M.Merz, and C.A.Fierke (1996).
Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer.
  Biochemistry, 35, 16421-16428.  
8987974 L.R.Scolnick, and D.W.Christianson (1996).
X-ray crystallographic studies of alanine-65 variants of carbonic anhydrase II reveal the structural basis of compromised proton transfer in catalysis.
  Biochemistry, 35, 16429-16434.
PDB codes: 1uga 1ugb 1ugc 1ugd 1uge 1ugf 1ugg
8634241 L.S.Brinen, W.S.Willett, C.S.Craik, and R.J.Fletterick (1996).
X-ray structures of a designed binding site in trypsin show metal-dependent geometry.
  Biochemistry, 35, 5999-6009.
PDB codes: 1slu 1slv 1slw 1slx
8723315 P.G.Artz, K.G.Valentine, S.J.Opella, and P.Lu (1996).
Lac repressor-operator interaction: N-terminal peptide backbone 1H and 15N chemical shifts upon complex formation with DNA.
  J Mol Recognit, 9, 13-22.  
7761440 J.A.Ippolito, T.T.Baird, S.A.McGee, D.W.Christianson, and C.A.Fierke (1995).
Structure-assisted redesign of a protein-zinc-binding site with femtomolar affinity.
  Proc Natl Acad Sci U S A, 92, 5017-5021.
PDB codes: 1ccs 1cct 1ccu
  8535241 P.Shih, D.R.Holland, and J.F.Kirsch (1995).
Thermal stability determinants of chicken egg-white lysozyme core mutants: hydrophobicity, packing volume, and conserved buried water molecules.
  Protein Sci, 4, 2050-2062.
PDB codes: 1lsm 1lsn
7656045 M.L.Mansfield (1994).
Are there knots in proteins?
  Nat Struct Biol, 1, 213-214.  
8477723 S.K.Nair, and D.W.Christianson (1993).
Crystallographic studies of azide binding to human carbonic anhydrase II.
  Eur J Biochem, 213, 507-515.  
7901850 Y.Xue, A.Liljas, B.H.Jonsson, and S.Lindskog (1993).
Structural analysis of the zinc hydroxide-Thr-199-Glu-106 hydrogen-bond network in human carbonic anhydrase II.
  Proteins, 17, 93.
PDB codes: 1cai 1caj 1cak 1cal 1cam
1368433 C.Eigenbrot, and A.A.Kossiakoff (1992).
Structural consequences of mutation.
  Curr Opin Biotechnol, 3, 333-337.  
1323835 N.X.Krueger, and H.Saito (1992).
A human transmembrane protein-tyrosine-phosphatase, PTP zeta, is expressed in brain and has an N-terminal receptor domain homologous to carbonic anhydrases.
  Proc Natl Acad Sci U S A, 89, 7417-7421.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.